2GM2
NMR structure of Xanthomonas campestris XCC1710: Northeast Structural Genomics Consortium target XcR35
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 3D_15N-separated_NOESY | 0.5 mM XCC1710 | pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 5% D2O | 100 mM NaCl, 20 mM CaCl2 | 6.5 | ambient | 298 | |
2 | 3D_13C-separated_NOESY | 0.5 mM XCC1710 | pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 5% D2O | 100 mM NaCl, 20 mM CaCl2 | 6.5 | ambient | 298 | |
3 | 3D_13C-separated_NOESY | 0.5 mM XCC1710 | pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 100% D2O | 100 mM NaCl, 20 mM CaCl2 | 6.5 | ambient | 298 | |
4 | 4D_13C-separated_NOESY | 0.5 mM XCC1710 | pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 100% D2O | 100 mM NaCl, 20 mM CaCl2 | 6.5 | ambient | 298 | |
5 | HNHA | 0.5 mM XCC1710 | pH 6.5 MES, 100 mM NaCl, 20 mM CaCl2, 10 mM DTT, 0.02% NaN3, 5% D2O | 100 mM NaCl, 20 mM CaCl2 | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | UNITYPLUS | 500 |
2 | Varian | INOVA | 600 |
3 | Varian | INOVA | 750 |
NMR Refinement | ||
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Method | Details | Software |
THE INITIAL STRUCTURE WAS DETERMINED USING AUTOMATED STRUCTURE DETERMINATION (AUTOSTRUCTURE) AND REFINED MANUALLY. A FINAL REFINEMENT USED SIMULTATED ANNEALING IN EXPLICIT SOLVENT. | THE STRUCTURES ARE BASED ON A TOTAL OF 935 RESTRAINTS. SUMMARY OF EXPERIMENTAL CONSTRAINTS RESTRAINING DISTANCE RESTRAINTS: TOTAL = 758; INTRA-RESIDUE [I=J] = 174; SEQUENTIAL [(I-J)=1] = 174; MEDIUM RANGE [1<(I-J)<5] = 109; LONG RANGE [(I-J)>=5] = 301; HYDROGEN BOND RESTRAINTS = 56 (2 PER H-BOND); NUMBER OF RESTRAINING DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 7.3; DIHEDRAL-ANGLE RESTRAINTS = 121 (60 PHI, 59 PSI, 2 CHI-1); TOTAL NUMBER OF RESTRAINTS PER RESTRAINED RESIDUE = 8.3; NUMBER OF LONG RANGE NOE DISTANCE RESTRAINTS PER RESTRAINED RESIDUE = 2.7; NUMBER OF STRUCTURES COMPUTED = 40; NUMBER OF STRUCTURES USED = 20; AVERAGE DISTANCE VIOLATIONS >0.0001 ANG = 19.8 +/- 3.5; AVERAGE R.M.S. DISTANCE VIOLATION = 0.0009 +/- 0.0003 ANG; MAXIMUM NUMBER OF DISTANCE VIOLATIONS 25; MAXIMUM DISTANCE VIOLATION = 0.03 ANG; AVERAGE DIHEDRAL ANGLE VIOLATIONS: >0.0001 DEG = 2.5+/-1.3; MAX NUMBER OF DIHEDRAL ANGLE VIOLATIONS = 4; AVERAGE R.M.S. DIHEDRAL ANGLE VIOLATION = 0.02 +/- .01 DEG.; RMSD VALUES TO AVERAGE STRUCTURE: BACKBONE ATOMS (N,C,C' RESIDUES 12-125) = 0.88 ANG, ALL HEAVY ATOMS = 1.38 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 32-122) = 0.71 ANG, ALL HEAVY ATOMS = 1.21 ANG; BACKBONE ATOMS (N,C,C' RESIDUES 16-17,21-36,39-41,44-46,53-73,76-122) = 0.70 ANG, ALL HEAVY ATOMS = 1.14 ANG; PROCHECK (RESIDUES 16-17,21-36,39-41,44-46,53-73,76-122): MOST FAVORED REGIONS = 84.6%; ADDITIONAL ALLOWED REGIONS = 14.0%; GENEROUSLY ALLOWED REGIONS = 0.2%; DISALLOWED REGIONS = 1.2%; PROCHECK (RESIDUES 12-125): MOST FAVORED REGIONS = 77.8%; ADDITIONAL ALLOWED REGIONS = 19.2%; GENEROUSLY ALLOWED REGIONS = 2.0%; DISALLOWED REGIONS = 1.0%. | VNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with fewest restraint violations, low restraint violation energies, and acceptable geometry |
Conformers Calculated Total Number | 40 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | VNMR | 6.1.C | Varian |
2 | processing | Felix | 98 | MSI |
3 | data analysis | Sparky | 3.106 | T.D. Goddard & D.G. Kneller |
4 | structure solution | AutoStructure | 2.1.1 | G.T. Montelione & J. Huang |
5 | structure solution | X-PLOR | NIH | A. Brunger et al |
6 | structure solution | CNS | 1.1 | A. Brunger et al |
7 | refinement | CNS | 1.1 | A. Brunger et al |